Pub Date : 2023-06-30DOI: 10.15625/1811-4989/18607
Mai Thi Phuong Nga, Nguyen Thi Thuy Linh, To Thi Mai Huong
Rice bran oil is becoming more and more popular plant oil source for human consumption. As one of the biggest producers of rice worldwide, the regulation of rice bran oil contained in Vietnam is becoming more necessary. In the present study, 161 rice accessions, which derive from diverse ecosystems in Vietnam, were used to investigate their palmitic acid (PA) content, the significant Single Nucleotide Polymorphisms (SNPs) as well as candidate genes relating to PA content using genome-wide association studies (GWAS). From the GWAS analysis, sixty-two noteworthy markers and nine quantitative trait loci were detected on chromosomes 1 and 11. Moreover, 187 candidate genes were identified. Notably, we identified the candidate genes including OsFAD and GDSL-like lipase/acylhydrolase, whose function relates to fatty acid (FA) content. Furthermore, the LOC_Os11g27370.1 gene, which encodes UDP-glucuronosyltransferase domain-containing protein, located on qC16.0.11.6, chromosome 11, has been involved in the FA biosynthesis pathway in animals but has not been proven yet in plants. Therefore, this gene could serve as a potential candidate gene to validate its function in rice plants. Other candidate genes with diverse functions were identified from our study but the relation to FA biosynthesis pathway has not been proven yet in any other studies. Therefore, these candidate genes can also open a number of in-depth studies to validate their involvement in FA biosynthesis pathways. The results from this study not only give a deeper knowledge of PA in rice bran oil but also pave the way for future applications in breeding programs aimed at improving the oil profile in rice.
米糠油越来越多地成为人类食用的植物油来源。作为世界上最大的水稻生产国之一，对越南米糠油含量的监管变得越来越有必要。本研究利用来自越南不同生态系统的 161 个水稻品种，通过全基因组关联研究（GWAS）调查了它们的棕榈酸（PA）含量、重要的单核苷酸多态性（SNPs）以及与 PA 含量相关的候选基因。通过全基因组关联研究（GWAS）分析，在 1 号和 11 号染色体上发现了 62 个值得注意的标记和 9 个数量性状位点。此外，还发现了 187 个候选基因。值得注意的是，我们发现的候选基因包括 OsFAD 和 GDSL 样脂肪酶/酰基水解酶，其功能与脂肪酸（FA）含量有关。此外，位于第 11 号染色体 qC16.0.11.6 上的 LOC_Os11g27370.1 基因编码含 UDP-葡萄糖醛酸基转移酶结构域的蛋白，该基因在动物中参与了脂肪酸的生物合成途径，但在植物中尚未得到证实。因此，该基因可作为潜在的候选基因，以验证其在水稻植物中的功能。我们的研究还发现了其他具有不同功能的候选基因，但这些基因与 FA 生物合成途径的关系尚未在其他研究中得到证实。因此，这些候选基因还可以开启一系列深入研究，以验证它们在 FA 生物合成途径中的参与。本研究的结果不仅加深了人们对米糠油中 PA 的认识，还为今后应用于旨在改善水稻油脂特征的育种计划铺平了道路。
{"title":"Genome-wide association studies for identification of genes and QTLs controlling the palmitic acid content in rice bran oil","authors":"Mai Thi Phuong Nga, Nguyen Thi Thuy Linh, To Thi Mai Huong","doi":"10.15625/1811-4989/18607","DOIUrl":"https://doi.org/10.15625/1811-4989/18607","url":null,"abstract":"Rice bran oil is becoming more and more popular plant oil source for human consumption. As one of the biggest producers of rice worldwide, the regulation of rice bran oil contained in Vietnam is becoming more necessary. In the present study, 161 rice accessions, which derive from diverse ecosystems in Vietnam, were used to investigate their palmitic acid (PA) content, the significant Single Nucleotide Polymorphisms (SNPs) as well as candidate genes relating to PA content using genome-wide association studies (GWAS). From the GWAS analysis, sixty-two noteworthy markers and nine quantitative trait loci were detected on chromosomes 1 and 11. Moreover, 187 candidate genes were identified. Notably, we identified the candidate genes including OsFAD and GDSL-like lipase/acylhydrolase, whose function relates to fatty acid (FA) content. Furthermore, the LOC_Os11g27370.1 gene, which encodes UDP-glucuronosyltransferase domain-containing protein, located on qC16.0.11.6, chromosome 11, has been involved in the FA biosynthesis pathway in animals but has not been proven yet in plants. Therefore, this gene could serve as a potential candidate gene to validate its function in rice plants. Other candidate genes with diverse functions were identified from our study but the relation to FA biosynthesis pathway has not been proven yet in any other studies. Therefore, these candidate genes can also open a number of in-depth studies to validate their involvement in FA biosynthesis pathways. The results from this study not only give a deeper knowledge of PA in rice bran oil but also pave the way for future applications in breeding programs aimed at improving the oil profile in rice.","PeriodicalId":23622,"journal":{"name":"Vietnam Journal of Biotechnology","volume":"17 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139367514","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-30DOI: 10.15625/1811-4989/18370
Le Tho Son, Bui Thi Mai Huong, Ha Bich Hong, Nguyen Thi Thu
Halicephalobus nematodes are parasites in horses, ruminants, and humans. They with the most demonstrated H. gingivalis infect the hosts and cause granulomas to fatalities. Anthelmintic treatments are not effective in many cases, so precautions against Halicephalobus infection based on the understanding of life history may help. So far, ten species have been globally identified. We isolated many wild-type Halicephalobus sp. strains in vegetation samples collected from two national parks (Cat Tien and Cuc Phuong National Parks) in Vietnam and cultured them on bacteria. Thus, Halicephalobus nematodes could live in the wild and feed on bacteria. In previous studies, horses were predominantly found to be hosts of Halicephalobus sp. nematodes, but in this study they are not presented in the parks, suggesting that other wild animals such as ruminants in the parks should be their hosts. In addition, we analyzed the 18S rDNA sequences of the isolated nematodes and found that they are likely divergent between the two ecological systems, suggesting the two nematode communities have evolved differently.
{"title":"The abundance of parasitic nematodes Halicephalobus species (Nematoda: Rhabditida) invading humans and animals in national parks of Vietnam","authors":"Le Tho Son, Bui Thi Mai Huong, Ha Bich Hong, Nguyen Thi Thu","doi":"10.15625/1811-4989/18370","DOIUrl":"https://doi.org/10.15625/1811-4989/18370","url":null,"abstract":"Halicephalobus nematodes are parasites in horses, ruminants, and humans. They with the most demonstrated H. gingivalis infect the hosts and cause granulomas to fatalities. Anthelmintic treatments are not effective in many cases, so precautions against Halicephalobus infection based on the understanding of life history may help. So far, ten species have been globally identified. We isolated many wild-type Halicephalobus sp. strains in vegetation samples collected from two national parks (Cat Tien and Cuc Phuong National Parks) in Vietnam and cultured them on bacteria. Thus, Halicephalobus nematodes could live in the wild and feed on bacteria. In previous studies, horses were predominantly found to be hosts of Halicephalobus sp. nematodes, but in this study they are not presented in the parks, suggesting that other wild animals such as ruminants in the parks should be their hosts. In addition, we analyzed the 18S rDNA sequences of the isolated nematodes and found that they are likely divergent between the two ecological systems, suggesting the two nematode communities have evolved differently.","PeriodicalId":23622,"journal":{"name":"Vietnam Journal of Biotechnology","volume":"7 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136369846","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-30DOI: 10.15625/1811-4989/18344
Tran Thi Hoa, Nguyen Thu Giang, Nguyen Thi Hong Ha, Tran Thi Huyen, Do Tien Phat, Chu Hoang Ha, Pham Bich Ngoc, Tran Ho Quang
Plant endophytes are an interesting group of microorganisms that colonize the internal tissues of living plants and do not cause any disease symptoms in the host plant. It exists in different parts of plants, such as roots, leaves, and stems, and significantly affects the formation of metabolic products in plants by promoting the accumulation of important secondary metabolites. The present study focused on analyzing the diversity and distribution of endophytic fungi related to different tissues from samples of the medicinal plant Dysosma difformis (Hemsl & E.H. Wilson) T.H. Wang collected in Ha Giang and Lai Chau, in which the isolates from roots were 27 strains (50.94%), 12 strains from stems (22.64%), and 14 strains from leaves (26.42%). Based on the isolates, we analyzed the fungal diversity through seven different diversity indices. The results showed that isolates’ diversity was similar to the endophytic fungal population in tissues of D. difformis distributed in different vegetation in Vietnam. Specifically, Shannon's index showed the highest diversity in roots (H′ = 2.673), followed by stems (H′ = 2.162) and leaves (H′ = 2,054). Similarly, species richness was highest in roots (Dmg = 4,551; Dmn = 3,079) and stem (Dmg = 4,024; Dmn = 3,175) and lowest in leaves (Dmg = 3.41; Dmn = 2,405). However, the Simpson diversity index showed that the endophytic fungal community was most abundance in leaves (1-D = 0.911), followed by stems (1-D = 0.897) and roots (1-D = 0.867). In addition, the Sorensen index of 0.615 shows the average similarity in species composition between the two sites, Ha Giang and Lai Chau. This is the first report on the diversity of endophytic fungi isolated from D. difformis, paving a potential way for screening endogenous fungal strains capable of producing important secondary compounds.
{"title":"Diversity of endophytic fungi from medicinal plants Dysosma difformis (Hemsl & E.H. Wilson) T.H. Wang collected in Ha Giang and Lai Chau.","authors":"Tran Thi Hoa, Nguyen Thu Giang, Nguyen Thi Hong Ha, Tran Thi Huyen, Do Tien Phat, Chu Hoang Ha, Pham Bich Ngoc, Tran Ho Quang","doi":"10.15625/1811-4989/18344","DOIUrl":"https://doi.org/10.15625/1811-4989/18344","url":null,"abstract":"Plant endophytes are an interesting group of microorganisms that colonize the internal tissues of living plants and do not cause any disease symptoms in the host plant. It exists in different parts of plants, such as roots, leaves, and stems, and significantly affects the formation of metabolic products in plants by promoting the accumulation of important secondary metabolites. The present study focused on analyzing the diversity and distribution of endophytic fungi related to different tissues from samples of the medicinal plant Dysosma difformis (Hemsl & E.H. Wilson) T.H. Wang collected in Ha Giang and Lai Chau, in which the isolates from roots were 27 strains (50.94%), 12 strains from stems (22.64%), and 14 strains from leaves (26.42%). Based on the isolates, we analyzed the fungal diversity through seven different diversity indices. The results showed that isolates’ diversity was similar to the endophytic fungal population in tissues of D. difformis distributed in different vegetation in Vietnam. Specifically, Shannon's index showed the highest diversity in roots (H′ = 2.673), followed by stems (H′ = 2.162) and leaves (H′ = 2,054). Similarly, species richness was highest in roots (Dmg = 4,551; Dmn = 3,079) and stem (Dmg = 4,024; Dmn = 3,175) and lowest in leaves (Dmg = 3.41; Dmn = 2,405). However, the Simpson diversity index showed that the endophytic fungal community was most abundance in leaves (1-D = 0.911), followed by stems (1-D = 0.897) and roots (1-D = 0.867). In addition, the Sorensen index of 0.615 shows the average similarity in species composition between the two sites, Ha Giang and Lai Chau. This is the first report on the diversity of endophytic fungi isolated from D. difformis, paving a potential way for screening endogenous fungal strains capable of producing important secondary compounds.","PeriodicalId":23622,"journal":{"name":"Vietnam Journal of Biotechnology","volume":"30 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139366612","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-30DOI: 10.15625/1811-4989/18256
Vu Thi Tien, Le Hoang Duc, Bui Van Ngoc, Nguyen Trung Nam
Breast cancer is the most frequently diagnosed cancer in women globally. The tumor microenvironment plays a vital role in epithelial-to-mesenchymal transition (EMT), leading to the invasion and metastasis of cancer cells. The tumor microenvironment includes all components of the tumor cells, including the extracellular matrix, tumor vasculature, mesenchymal stem cells, immune cells, and fibroblasts. Understanding the interactions between mesenchymal stem cells and cancer cells is essential in determining the role of mesenchymal stem cells in diagnosing and treating breast cancer. In this study, we present the result of co-culture between adipose tissue mesenchymal stem cells (ADMSCs) and breast cancer cells (MCF-7 cell line) and determine the expression levels of transcription factors involved in EMT, including Twist and Snail. The results showed that the proliferation of MCF-7 co-cultured with ADMSCs was not increased compared to MCF-7 mono-cultured. Determination of gene expression levels by qRT-PCR revealed a significant increase in the EMT-related transcription factors (Twist and Snail) in breast cancer cells upon co-culture with ADMSCs. There were also significant differences between the expression levels of IL-6 and AhR in MCF-7 cells co-cultured with ADMSCs and MCF-7 cells mono-cultured. The results suggested that ADMSCs promoted the EMT of MCF-7 cells, potentially via AhR/NF-κB pathways.
{"title":"Expression of transcription factors involved in epithelial-to-mesenchymal transition of the breast cancer cell line MCF-7 co-cultured with adipose tissue mesenchymal stem cells","authors":"Vu Thi Tien, Le Hoang Duc, Bui Van Ngoc, Nguyen Trung Nam","doi":"10.15625/1811-4989/18256","DOIUrl":"https://doi.org/10.15625/1811-4989/18256","url":null,"abstract":"Breast cancer is the most frequently diagnosed cancer in women globally. The tumor microenvironment plays a vital role in epithelial-to-mesenchymal transition (EMT), leading to the invasion and metastasis of cancer cells. The tumor microenvironment includes all components of the tumor cells, including the extracellular matrix, tumor vasculature, mesenchymal stem cells, immune cells, and fibroblasts. Understanding the interactions between mesenchymal stem cells and cancer cells is essential in determining the role of mesenchymal stem cells in diagnosing and treating breast cancer. In this study, we present the result of co-culture between adipose tissue mesenchymal stem cells (ADMSCs) and breast cancer cells (MCF-7 cell line) and determine the expression levels of transcription factors involved in EMT, including Twist and Snail. The results showed that the proliferation of MCF-7 co-cultured with ADMSCs was not increased compared to MCF-7 mono-cultured. Determination of gene expression levels by qRT-PCR revealed a significant increase in the EMT-related transcription factors (Twist and Snail) in breast cancer cells upon co-culture with ADMSCs. There were also significant differences between the expression levels of IL-6 and AhR in MCF-7 cells co-cultured with ADMSCs and MCF-7 cells mono-cultured. The results suggested that ADMSCs promoted the EMT of MCF-7 cells, potentially via AhR/NF-κB pathways.","PeriodicalId":23622,"journal":{"name":"Vietnam Journal of Biotechnology","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136368603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-30DOI: 10.15625/1811-4989/18124
Nguyen Thy Ngoc, Ha Manh Quyet
Primary myelofibrosis is the severe form of myeloproliferative neoplasms that causes scar tissue in the bone marrow, leading to low production of blood cells and thus, life span shortening. Besides the most common variant JAK2 V617F, the association between these disorders with other variants in the JAK2 gene, especially the exon 12 variants have been poorly studied. In our research, the JAK2 exon 12 variants were detected by amplification and sequencing from genomic samples of five cases with V617F-negative primary myelofibrosis. Results showed that among 5/14 primary myelofibrosis patients with V617F-negative profile, only two patients carried exon 12 variants (JAK2 c.1592A>G p.H531R, and c.1613A>C p.H538P). In silico analysis indicated that the variant c.1613A>C p.H538P was novel and potentially pathogenic. The positioning demonstration by Missense3D tools indicated that this variant localized in the proximity to the pathogenic variant V617F, suggesting a potential effect on the enzymatic activity of Janus kinase 2. This initial data can be used as a genetic diagnostic criterion for myeloproliferative neoplasms. Nonetheless, the effect of p.H538P needs to be verified by further investigations.
{"title":"JAK2 exon 12 variants in vietnamese patients with JAK2 V617F-negative primary myelofibrosis","authors":"Nguyen Thy Ngoc, Ha Manh Quyet","doi":"10.15625/1811-4989/18124","DOIUrl":"https://doi.org/10.15625/1811-4989/18124","url":null,"abstract":"Primary myelofibrosis is the severe form of myeloproliferative neoplasms that causes scar tissue in the bone marrow, leading to low production of blood cells and thus, life span shortening. Besides the most common variant JAK2 V617F, the association between these disorders with other variants in the JAK2 gene, especially the exon 12 variants have been poorly studied. In our research, the JAK2 exon 12 variants were detected by amplification and sequencing from genomic samples of five cases with V617F-negative primary myelofibrosis. Results showed that among 5/14 primary myelofibrosis patients with V617F-negative profile, only two patients carried exon 12 variants (JAK2 c.1592A>G p.H531R, and c.1613A>C p.H538P). In silico analysis indicated that the variant c.1613A>C p.H538P was novel and potentially pathogenic. The positioning demonstration by Missense3D tools indicated that this variant localized in the proximity to the pathogenic variant V617F, suggesting a potential effect on the enzymatic activity of Janus kinase 2. This initial data can be used as a genetic diagnostic criterion for myeloproliferative neoplasms. Nonetheless, the effect of p.H538P needs to be verified by further investigations.","PeriodicalId":23622,"journal":{"name":"Vietnam Journal of Biotechnology","volume":"10 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136368605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-22DOI: 10.15625/1811-4989/17647
T. T. Tran, H. S. Tran, B. T. Le, S. Nguyen, H. Vu, O. Kim
Insulin-like growth factor binding protein 5 (IGFBP5) is the highest conserved member of IGFBP family, and has the broad range of biological activities effecting on the cell growth. This study aims to investigate the association between genetic variation in IGFBP5 gene and the growth of striped catfish (Pangasianodon hypophthalmus). Single nucleotide polymorphisms (SNPs) were discovered and validated in IGFBP5 gene from two growth-selected populations (fast- and slow- growing fish). For SNP discovery, the fragments of IGFBP5 from sample sets of 10 fast- growing fish and 10 slow- growing fish were directly sequenced by Sanger sequencing. In this stage, 4 exonic SNPs were discovered, including a non-synonymous SNP 525 T>A (p. Val16Glu) in exon 1, and three synonymous SNPs (8859 G>A, 11713 C>A, 11992 T>C) in exon 4. The non-synonymous SNP 525 T>A (p.Val16Glu) was filtered to the next step of SNP validation. For validation, the SNP was individually genotyped in the test populations of 70 fast- growing fish and 70 slow- growing fish by single base extension method. Data analysis from the total SNPs which were collected from 80 fast- growing fish and 80 slow- growing fish indicated that non-synonymous SNP 525 T>A (p.Val16Glu) was significantly associated to the growth of striped catfish (p-value <0.001). Analysis of genetic diversity parameters (PIC, MAF) suggested that this SNP is a common variant, contributes significantly to the genetic variance. The non-synonymous SNP 525 T>A (p.Val16Glu) in IGFBP5 gene would become a SNP marker candidate for marker assisted selection (MAS) that can be used in pangasius breeding.
胰岛素样生长因子结合蛋白5 (IGFBP5)是IGFBP家族中最保守的成员，具有广泛的影响细胞生长的生物活性。本研究旨在探讨IGFBP5基因的遗传变异与斑纹鲶鱼(Pangasianodon hypophthalmus)生长的关系。在两个生长选择种群(快生长和慢生长)中发现并验证了IGFBP5基因的单核苷酸多态性(snp)。为了发现SNP，我们直接对10条快生长鱼和10条慢生长鱼的IGFBP5片段进行了Sanger测序。在这个阶段，发现了4个外显子SNP，包括1号外显子的非同义SNP 525 T> a (p. Val16Glu)和4号外显子的3个同义SNP (8859 G> a, 11713 C> a, 11992 T>C)。非同义SNP 525 T>A (p.Val16Glu)被过滤到SNP验证的下一步。为了验证该SNP，我们用单碱基延伸法对70条快生长鱼和70条慢生长鱼的测试群体进行了基因分型。对80条快生长鱼和80条慢生长鱼的总SNP数据分析表明，非同义SNP 525 T>A (p.Val16Glu)与条纹鲶鱼的生长显著相关，IGFBP5基因的p值A (p.Val16Glu)将成为标记辅助选择(MAS)的SNP候选标记，可用于巴鲶鱼育种。
{"title":"Significant association between a non-synonymous snp in IGFBP5 gene and the growth of striped catfish (Pangasianodon hypophthalmus, Sauvage, 1878)","authors":"T. T. Tran, H. S. Tran, B. T. Le, S. Nguyen, H. Vu, O. Kim","doi":"10.15625/1811-4989/17647","DOIUrl":"https://doi.org/10.15625/1811-4989/17647","url":null,"abstract":"Insulin-like growth factor binding protein 5 (IGFBP5) is the highest conserved member of IGFBP family, and has the broad range of biological activities effecting on the cell growth. This study aims to investigate the association between genetic variation in IGFBP5 gene and the growth of striped catfish (Pangasianodon hypophthalmus). Single nucleotide polymorphisms (SNPs) were discovered and validated in IGFBP5 gene from two growth-selected populations (fast- and slow- growing fish). For SNP discovery, the fragments of IGFBP5 from sample sets of 10 fast- growing fish and 10 slow- growing fish were directly sequenced by Sanger sequencing. In this stage, 4 exonic SNPs were discovered, including a non-synonymous SNP 525 T>A (p. Val16Glu) in exon 1, and three synonymous SNPs (8859 G>A, 11713 C>A, 11992 T>C) in exon 4. The non-synonymous SNP 525 T>A (p.Val16Glu) was filtered to the next step of SNP validation. For validation, the SNP was individually genotyped in the test populations of 70 fast- growing fish and 70 slow- growing fish by single base extension method. Data analysis from the total SNPs which were collected from 80 fast- growing fish and 80 slow- growing fish indicated that non-synonymous SNP 525 T>A (p.Val16Glu) was significantly associated to the growth of striped catfish (p-value <0.001). Analysis of genetic diversity parameters (PIC, MAF) suggested that this SNP is a common variant, contributes significantly to the genetic variance. The non-synonymous SNP 525 T>A (p.Val16Glu) in IGFBP5 gene would become a SNP marker candidate for marker assisted selection (MAS) that can be used in pangasius breeding.","PeriodicalId":23622,"journal":{"name":"Vietnam Journal of Biotechnology","volume":"113 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91415879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-28DOI: 10.15625/1811-4989/17053
Tran Thi Ngoc Thu, Nguyen Thi Dong Phuong, Tran Van Luan, Le Thi Van Anh
Microalgal harvesting has still been a challenge to investigators who take their investiment into microalgal production. The cost for microalgal downstream processing is as high as 20% of the total production of biodiesel. Among hundreds of curent methods of biomass harvesting, autoflocculation and bacteria-based aggregation are still being researched and applied in large-scale producuion. This study implemented a comparison of how microalgal cells aggregate large bioflocs according to two types of flocculation. The microalgal autoflocculation was implemented by adding Ca2+ or Mg2+ with an increase of pH to 11, resulting in cell biomass of 13.7 or 15.5 mg/l, respectively. Meanwhile, the bioflocculation under the support of Bacillus subtilis MT300405 and Escherichia coli ATCC 85922 could produce large bioflocs with a cell biomass of 1.5 times higher than the autoflocculation case without the influence of pH. Moreover, images from scanning electron microscopy indicated differences between two types of flocculation. With the presence of bacteria, microalgal cells were more tightly bound by a membrane or a layer of extracellular polimeric substance, inducing to form large bioflocs. This was not found under autoflocculation.
{"title":"Comparison of biofloc formation from microalgal cultivation by auto- and bacteria-associated types of flocculation","authors":"Tran Thi Ngoc Thu, Nguyen Thi Dong Phuong, Tran Van Luan, Le Thi Van Anh","doi":"10.15625/1811-4989/17053","DOIUrl":"https://doi.org/10.15625/1811-4989/17053","url":null,"abstract":"Microalgal harvesting has still been a challenge to investigators who take their investiment into microalgal production. The cost for microalgal downstream processing is as high as 20% of the total production of biodiesel. Among hundreds of curent methods of biomass harvesting, autoflocculation and bacteria-based aggregation are still being researched and applied in large-scale producuion. This study implemented a comparison of how microalgal cells aggregate large bioflocs according to two types of flocculation. The microalgal autoflocculation was implemented by adding Ca2+ or Mg2+ with an increase of pH to 11, resulting in cell biomass of 13.7 or 15.5 mg/l, respectively. Meanwhile, the bioflocculation under the support of Bacillus subtilis MT300405 and Escherichia coli ATCC 85922 could produce large bioflocs with a cell biomass of 1.5 times higher than the autoflocculation case without the influence of pH. Moreover, images from scanning electron microscopy indicated differences between two types of flocculation. With the presence of bacteria, microalgal cells were more tightly bound by a membrane or a layer of extracellular polimeric substance, inducing to form large bioflocs. This was not found under autoflocculation.","PeriodicalId":23622,"journal":{"name":"Vietnam Journal of Biotechnology","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73208658","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-28DOI: 10.15625/1811-4989/17310
Huynh Thi Thu Hue, Le Quynh Lien, Nguyen Chi Mai, Tran My Linh, Bui Manh Minh
Dehydrin is a large protein group to have protective functions to plant cells under osmotic stress. Overexpression of dehydrin encoded genes isolated from mangrove plants had improved drought tolerance of transgenic plants. Therefore, in this research, a coding sequence with the length of 573bp that encodes Dehydrin1 (DH1) protein was isolated from a mangrove plant namely Mam bien (Avicennia marina) which naturally grows in Xuan Thuy national park, Vietnam. The coding sequence was denoted as AmDH1 and cloned into the plant transformation vector pCAM 35S-AmDH1. The transgenic vector was transformed into A. tumefiaciens cells and the vector was transferred into the K7 maize line to generate transgenic maize seedlings. The AmDH1 transgenic maize T2 seedlings have shown an improved drought tolerance than the original K7 maize line.
脱氢蛋白是一种对植物细胞在渗透胁迫下具有保护作用的大蛋白群。从红树林植物中分离的过表达脱氢编码基因提高了转基因植物的抗旱性。因此，本研究从越南宣翠国家公园天然生长的红树林植物Mam bien (Avicennia marina)中分离出一个编码Dehydrin1 (DH1)蛋白的编码序列，全长573bp。编码序列命名为AmDH1，将其克隆到植物转化载体pCAM 35S-AmDH1中。将该转基因载体转化为A. tummefiaciens细胞，并将其转入K7玉米株系，获得转基因玉米幼苗。AmDH1转基因玉米T2幼苗的抗旱性比原玉米K7株系有所提高。
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Pub Date : 2023-03-22DOI: 10.15625/1811-4989/17967
Le Thi Van Anh, Mai Thi Phuong Nga, Tran Thi Phuong Linh, Nguyen Minh Anh, Huynh Thi Phuong Linh, Nguyen Chi Thanh, Le Thi Thu Phuong, Nguyen Thi Kieu Oanh
Histological analysis, which aims to investigate the microscopic anatomy of biological tissues, has been a simple and powerful technique for plant taxonomy. Sectioning followed by staining methods is widely used in observing histological structures. However, the staining techniques often destroy tissue and provide low-quality images due to nonspecific reactions with the dyes making further analysis difficult. In this report, we propose an applicable non-staining histology protocol based on auto-fluorescence characteristics of plant tissues and its application in the anatomical discrimination of six similar-appearance species of golden camellias as a case study. We compared the images from the same tissue under a bright field with the staining step and under fluorescence directly without the staining step in the sample preparation. The images were taken from Eclipse Ni-U microscopy (Nikon, Japan) with a color DS-Ri2 camera (Nikon, Japan) and NIS-ELEMENTS Basic Research Imaging software. The non-staining method demonstrated significant advantages compared to the staining protocol. The fluorescent images showed the distinction between adjacent leaf tissues with their own naturally reflective colors. In addition, the anatomical parameters, including the xylem area, phloem area, bundle sheath area, and palisade/spongy width ratio, were easily measured in good-quality images. These parameters were used in discriminative analysis by the Principal Component Analysis (PCA). The PCA diagram demonstrated the separation of six species, thus suggesting that these anatomical parameters can be used for taxonomy. In conclusion, our study showed a helpful technique in histological analysis that significantly contributes to the taxonomy of golden camellias species and can be applied in other plant varieties.
{"title":"Application of fluorescence microscopy for histological discrimination of golden camellias leaves","authors":"Le Thi Van Anh, Mai Thi Phuong Nga, Tran Thi Phuong Linh, Nguyen Minh Anh, Huynh Thi Phuong Linh, Nguyen Chi Thanh, Le Thi Thu Phuong, Nguyen Thi Kieu Oanh","doi":"10.15625/1811-4989/17967","DOIUrl":"https://doi.org/10.15625/1811-4989/17967","url":null,"abstract":"Histological analysis, which aims to investigate the microscopic anatomy of biological tissues, has been a simple and powerful technique for plant taxonomy. Sectioning followed by staining methods is widely used in observing histological structures. However, the staining techniques often destroy tissue and provide low-quality images due to nonspecific reactions with the dyes making further analysis difficult. In this report, we propose an applicable non-staining histology protocol based on auto-fluorescence characteristics of plant tissues and its application in the anatomical discrimination of six similar-appearance species of golden camellias as a case study. We compared the images from the same tissue under a bright field with the staining step and under fluorescence directly without the staining step in the sample preparation. The images were taken from Eclipse Ni-U microscopy (Nikon, Japan) with a color DS-Ri2 camera (Nikon, Japan) and NIS-ELEMENTS Basic Research Imaging software. The non-staining method demonstrated significant advantages compared to the staining protocol. The fluorescent images showed the distinction between adjacent leaf tissues with their own naturally reflective colors. In addition, the anatomical parameters, including the xylem area, phloem area, bundle sheath area, and palisade/spongy width ratio, were easily measured in good-quality images. These parameters were used in discriminative analysis by the Principal Component Analysis (PCA). The PCA diagram demonstrated the separation of six species, thus suggesting that these anatomical parameters can be used for taxonomy. In conclusion, our study showed a helpful technique in histological analysis that significantly contributes to the taxonomy of golden camellias species and can be applied in other plant varieties.","PeriodicalId":23622,"journal":{"name":"Vietnam Journal of Biotechnology","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89963840","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-12-28DOI: 10.15625/1811-4989/18221
The bacterial communities performing endophytic lifestyle have been proven to possess a number of characteristics useful to host plants and thus are considered as “plant probiotics”. Many probiotic bacteria were reported for antagonism against different plant pathogens, including bacteria, fungi, and nematodes. The use of endophytic bacteria as biocontrol agents would have great potentials, allowing reducing the use of agrochemicals and thus support a sustainable agriculture. In this study, endophytic bacteria isolated from rice plants of IR4625 cultivar from Long An province, Vietnam were used for screening strains that have antagonistic activity against Dickeya zeae (Dz), the bacterium causing foot rot disease. The rice plants had foot rot disease symptoms, i.e. dark-brown foot with odor smell typical for bacterial infection. Strain VY81 was isolated from a surface sterilized rice stem sample adjacent to the foot rot area. The crude extract of strain VY81 showed significant antagonistic activity against Dz, with the inhibition zone of 14,25 mm ± 1,06 in diameter. Strain VY81 produced the compound antagonizing Dz at maximal level after 48 h cultivated in TSB medium. The activity was found mainly in the culture broth, just a small part was found intracellularly. The bioactive compound antagonizing D. zeae produced by strain VY81 was purified by HPLC and analyzed by mass spectrometry and NMR spectroscopy. The compound was identified as a quinoline alkaloid, the chemical formula is C17H21ON with chemical name 2-(2-heptenyl)-3-methyl-4(1H)-quinolone. Comparative analyses of the 16S rDNA gene sequence revealed that strain VY81 belonged to the genus Burkholderia, most closely related to Burkholderia cepacia (99,77% sequence homology). The 16S rDNA sequence of strain VY81 was deposited at GenBank under accession number MW056196. Strain VY81 and its quinolone compound would have application potential for development of biocontrol product against the foot rot disease caused by Dickeya zeae.
{"title":"Isolation of rice endophytic bacterial strain VY81 and study on its bioactive compound antagonizing the phytopathogen Dickeya zeae","authors":"","doi":"10.15625/1811-4989/18221","DOIUrl":"https://doi.org/10.15625/1811-4989/18221","url":null,"abstract":"The bacterial communities performing endophytic lifestyle have been proven to possess a number of characteristics useful to host plants and thus are considered as “plant probiotics”. Many probiotic bacteria were reported for antagonism against different plant pathogens, including bacteria, fungi, and nematodes. The use of endophytic bacteria as biocontrol agents would have great potentials, allowing reducing the use of agrochemicals and thus support a sustainable agriculture. \u0000 In this study, endophytic bacteria isolated from rice plants of IR4625 cultivar from Long An province, Vietnam were used for screening strains that have antagonistic activity against Dickeya zeae (Dz), the bacterium causing foot rot disease. The rice plants had foot rot disease symptoms, i.e. dark-brown foot with odor smell typical for bacterial infection. Strain VY81 was isolated from a surface sterilized rice stem sample adjacent to the foot rot area. The crude extract of strain VY81 showed significant antagonistic activity against Dz, with the inhibition zone of 14,25 mm ± 1,06 in diameter. Strain VY81 produced the compound antagonizing Dz at maximal level after 48 h cultivated in TSB medium. The activity was found mainly in the culture broth, just a small part was found intracellularly. The bioactive compound antagonizing D. zeae produced by strain VY81 was purified by HPLC and analyzed by mass spectrometry and NMR spectroscopy. The compound was identified as a quinoline alkaloid, the chemical formula is C17H21ON with chemical name 2-(2-heptenyl)-3-methyl-4(1H)-quinolone. Comparative analyses of the 16S rDNA gene sequence revealed that strain VY81 belonged to the genus Burkholderia, most closely related to Burkholderia cepacia (99,77% sequence homology). The 16S rDNA sequence of strain VY81 was deposited at GenBank under accession number MW056196. Strain VY81 and its quinolone compound would have application potential for development of biocontrol product against the foot rot disease caused by Dickeya zeae.","PeriodicalId":23622,"journal":{"name":"Vietnam Journal of Biotechnology","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82397971","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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